SMTL ID : 2j9f.1

Human branched-chain alpha-ketoacid dehydrogenase-decarboxylase E1b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

hetero-2-2-mer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: E.193, N.222, Y.224 Ligands: THV.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.193, A:E.193, A:Y.224, H2O.12 MN.6: 4 residues within 4Å: Chain C: E.193, N.222, Y.224 Ligands: THV.8 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.193, C:E.193, C:Y.224, H2O.32

4 x K: POTASSIUM ION(Non-covalent)

K.2: 4 residues within 4Å: Chain A: S.161, P.163, T.166, Q.167 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.161, A:P.163, A:T.166, H2O.3 K.4: 7 residues within 4Å: Chain B: G.128, L.130, T.131, C.178, I.179, D.181, N.183 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:G.128, B:L.130, B:C.178, B:D.181, B:N.183 K.7: 4 residues within 4Å: Chain C: S.161, P.163, T.166, Q.167 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.161, C:S.161, C:P.163, H2O.25 K.9: 7 residues within 4Å: Chain D: G.128, L.130, T.131, C.178, I.179, D.181, N.183 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:G.128, D:C.178, D:D.181, D:N.183

2 x THV: C2-1-HYDROXY-3-METHYL-PROPYL-THIAMIN DIPHOSPHATE(Non-covalent)

THV.3: 26 residues within 4Å: Chain A: F.85, M.87, Q.112, Y.113, R.114, S.162, P.163, L.164, G.192, E.193, G.194, A.195, E.198, R.220, N.222, Y.224, A.225, I.226, H.291 Chain D: E.46, L.74, E.76, Q.98, Y.102, H.146 Ligands: MN.1 21 PLIP interactions: 18 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:F.85, A:Y.113, A:I.226, A:I.226, D:Y.102 Hydrogen bonds: A:Q.112, A:Y.113, A:S.162, A:G.192, A:G.192, A:G.194, A:A.195, A:H.291, D:Y.102 Water bridges: A:R.114, A:E.193, A:N.222, A:Y.224 Salt bridges: A:R.114, A:R.220 pi-Stacking: D:Y.102 THV.8: 25 residues within 4Å: Chain B: E.46, L.74, E.76, Q.98, Y.102, H.146 Chain C: F.85, Q.112, Y.113, R.114, S.162, P.163, L.164, G.192, E.193, G.194, A.195, E.198, R.220, N.222, Y.224, A.225, I.226, H.291 Ligands: MN.6 22 PLIP interactions: 20 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.85, C:Y.113, C:Y.113, C:I.226, C:I.226, B:Y.102 Hydrogen bonds: C:Q.112, C:Y.113, C:S.162, C:G.192, C:G.192, C:G.194, C:A.195, C:E.198, C:N.222 Water bridges: C:R.114, C:E.193, C:N.222 Salt bridges: C:R.114, C:R.220, C:H.291 pi-Stacking: B:Y.102

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: Q.374 Chain B: W.260, E.290, T.294, E.297 Chain D: L.283, T.284, R.309 8 PLIP interactions: 3 interactions with chain D, 5 interactions with chain B Hydrogen bonds: D:R.309, B:E.290, B:T.294, B:E.297 Water bridges: D:T.284, D:D.314, B:W.260, B:E.297 GOL.10: 7 residues within 4Å: Chain B: L.283, T.284, R.309 Chain C: Q.374 Chain D: W.260, E.290, T.294 9 PLIP interactions: 5 interactions with chain D, 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: D:E.290, D:T.294, D:E.297, B:T.284, B:R.309 Water bridges: D:W.260, D:E.298, B:T.284, C:Q.378 GOL.11: 7 residues within 4Å: Chain C: A.373, Q.374 Chain D: S.211, W.260, D.261, V.262, D.263 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:D.261, D:D.263, D:D.263, C:Q.374

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, J. et al., The Two Active Sites in Human Branched-Chain Alpha- Keto Acid Dehydrogenase Operate Independently without an Obligatory Alternating-Site Mechanism. J.Biol.Chem. (2007)

Release Date

2007-02-27

Peptides

2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT: AC
2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT

2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT